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Several Swiss cantons have exhausted their quotas of B permits available to specialist workers from non-EU countries wishing to work in Switzerland, it has emerged.

The canton of Geneva highlighted the issue in a letter to federal justice minister Simonetta Sommaruga this week, saying in a statement it was “extremely worried” that it could no longer offer the work permit to “highly qualified non-European specialists”.

Following the yes vote in the anti-immigration referendum of February 2014, the federal government reduced the number of permits available to non-EU – so-called ‘third state' – citizens in 2015 and 2016.

Geneva's prescribed quota for 2015 was only enough to cover the needs of third state workers because the federal migration office (SEM) was able to carry over some unused permits from 2014's quotas – held in a federal reserve – Geneva authorities said on Wednesday.

But this year Geneva had used up its quota of B permits (a renewable residency permit) by March, it said. And now the federal reserve is all gone too.

“The Senate is therefore no longer able to respond in a satisfactory manner to work permit applications lodged by companies in our canton.”

The situation will make new companies think twice about setting up in Geneva, it said, and risks companies already established there moving to places with more lenient conditions.

It is therefore asking the federal government to “very quickly take the decision” to raise the number of available permits for non-EU citizens.

Speaking to Le Tribune de Genève, Francois Longchamp, president of Geneva's government, said the cities of Basel and Zurich were in the same position.

The cantons will have to tell non-EU workers “to come back next year”, he said.

In 2014, Geneva had a quota of 451 B permits and 327 L permits (a short-term permit) to dish out, against this year's allocation of 307 and 167 respectively.

While this situation hits non-EU workers specifically, it will become a wider issue should Switzerland go ahead with implementing quotas on immigrants from EU countries.

The country has until February 2017 to find a way of honouring the 2014 anti-immigration initiative – which approved quotas on all immigration – whilst maintaining its relationship with the EU, which depends upon the free movement of people.

It is not yet clear how the issue of quotas will affect British nationals coming to live – or already living – in Switzerland once Britain leaves the EU and becomes a third state country.